aCharges

aCharges calculates partial atomic charges for protein structures in AlphaFoldDB to map electron distribution and inform chemical behavior and functional interpretation.

Key Features:

• Integration with AlphaFoldDB: Accesses over 200 million predicted protein structures in AlphaFoldDB, including complete organism proteomes such as human.
• Empirical charge calculation: Employs the SQE+qp empirical method parameterized for proteins using quantum mechanics charges from B3LYP/6-31G*/NPA calculations on PROPKA3-protonated structures.
• Data output: Produces partial atomic charges exportable in common data formats for integration into downstream bioinformatics workflows.

Scientific Applications:

• Chemical reactivity insights: Maps electron distribution to support analysis of enzyme mechanisms, ligand binding sites, and potential drug interactions.
• Functional annotation enhancement: Provides chemical behavior data to augment interpretation of predicted protein function and interactions.
• Proteomics research: Enables large-scale examination of proteomes for studies in comparative genomics, evolutionary biology, and systems biology.

Methodology:

Calculations apply the SQE+qp empirical method tailored for proteins, parameterized with quantum mechanics charges from B3LYP/6-31G*/NPA calculations on PROPKA3-protonated structures and integrated with AlphaFoldDB for processing predicted structures.